How to use samtools faidx

Question

[florian.grosmaire]

Hello everyone,

I would like to do a blast and then use the samtools faidx command in order to extract and align the hits from my blast. However, samtools faidx use an input in fasta format. My blast output is a text file.

Can someone help me ? Is there a way to convert a text file in fasta ? Thanks in advance

[Pierre Lindenbaum]

then use the samtools faidx command in order to extract and align the hits from my blast

this is the wrong tool. samtools faidx " indexes or queries regions from a fasta file ". For a start, you might use awk. For a very large file, import into a database.

[florian.grosmaire]

Thank you ! I understood where I was wrong . I will try something else. Instead of making a blast db I will try to make a biopython script that download sequences from ID's of the hits I get from my blast ouput

[GenoMax]

order to extract and align the hits from my blast.

Align to a reference? To each other like doing a multiple sequence alignment? As discussed in your recent thread blastdbcmd is appropriate to retrieve sequences from a blast database for further analysis.

[florian.grosmaire]

Thank you for your time and anwers !